npm - molstar - Versions diffs - 2.3.3 → 2.3.8 - Mend

molstar 2.3.3 → 2.3.8

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (1829) hide show

package/lib/commonjs/extensions/rcsb/validation-report/prop.js.map CHANGED Viewed

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1	- 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package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts CHANGED Viewed

@@ -16,12 +16,15 @@ export declare const IntraUnitClashParams: {
     sizeFactor: PD.Numeric;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
+    aromaticScale: PD.Numeric;
+    aromaticSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
     dashScale: PD.Numeric;
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
@@ -29,7 +32,7 @@ export declare const IntraUnitClashParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type IntraUnitClashParams = typeof IntraUnitClashParams;
 export declare function IntraUnitClashVisual(materialId: number): UnitsVisual<IntraUnitClashParams>;
@@ -38,12 +41,15 @@ export declare const InterUnitClashParams: {
     sizeFactor: PD.Numeric;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
+    aromaticScale: PD.Numeric;
+    aromaticSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
     dashScale: PD.Numeric;
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
@@ -51,17 +57,20 @@ export declare const InterUnitClashParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type InterUnitClashParams = typeof InterUnitClashParams;
 export declare function InterUnitClashVisual(materialId: number): ComplexVisual<InterUnitClashParams>;
 export declare const ClashesParams: {
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     visuals: PD.MultiSelect<"intra-clash" | "inter-clash">;
     linkCap: PD.BooleanParam;
     sizeFactor: PD.Numeric;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
+    aromaticScale: PD.Numeric;
+    aromaticSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
     dashScale: PD.Numeric;
     dashCap: PD.BooleanParam;
@@ -74,16 +83,19 @@ export declare const ClashesParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type ClashesParams = typeof ClashesParams;
 export declare function getClashesParams(ctx: ThemeRegistryContext, structure: Structure): {
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     visuals: PD.MultiSelect<"intra-clash" | "inter-clash">;
     linkCap: PD.BooleanParam;
     sizeFactor: PD.Numeric;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
+    aromaticScale: PD.Numeric;
+    aromaticSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
     dashScale: PD.Numeric;
     dashCap: PD.BooleanParam;
@@ -96,17 +108,20 @@ export declare function getClashesParams(ctx: ThemeRegistryContext, structure: S
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type ClashesRepresentation = StructureRepresentation<ClashesParams>;
 export declare function ClashesRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, ClashesParams>): ClashesRepresentation;
 export declare const ClashesRepresentationProvider: StructureRepresentationProvider<{
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     visuals: PD.MultiSelect<"intra-clash" | "inter-clash">;
     linkCap: PD.BooleanParam;
     sizeFactor: PD.Numeric;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
+    aromaticScale: PD.Numeric;
+    aromaticSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
     dashScale: PD.Numeric;
     dashCap: PD.BooleanParam;
@@ -119,5 +134,5 @@ export declare const ClashesRepresentationProvider: StructureRepresentationProvi
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 }, ValidationReport.Tag.Clashes>;

package/lib/commonjs/extensions/rcsb/validation-report/representation.js CHANGED Viewed

@@ -41,7 +41,7 @@ function createIntraUnitClashCylinderMesh(ctx, unit, structure, theme, props, me
             pos(elements[a[edgeIndex]], posA);
             pos(elements[b[edgeIndex]], posB);
         },
-        style: function (edgeIndex) { return 4 /* Disk */; },
+        style: function (edgeIndex) { return 6 /* Disk */; },
         radius: function (edgeIndex) { return magnitude[edgeIndex] * sizeFactor; },
     };
     return (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh);
@@ -78,7 +78,7 @@ function getIntraClashLabel(structure, unit, clashes, elements) {
     var mag = magnitude[idx].toFixed(2);
     var dist = distance[idx].toFixed(2);
     return [
-        "Clash id: " + id[idx] + " | Magnitude: " + mag + " \u212B | Distance: " + dist + " \u212B",
+        "Clash id: ".concat(id[idx], " | Magnitude: ").concat(mag, " \u212B | Distance: ").concat(dist, " \u212B"),
         (0, label_1.bondLabel)(structure_1.Bond.Location(structure, unit, clashes.a[idx], structure, unit, clashes.b[idx]))
     ].join('</br>');
 }
@@ -134,7 +134,7 @@ function createInterUnitClashCylinderMesh(ctx, structure, theme, props, mesh) {
             uA.conformation.position(uA.elements[b.indexA], posA);
             uB.conformation.position(uB.elements[b.indexB], posB);
         },
-        style: function (edgeIndex) { return 4 /* Disk */; },
+        style: function (edgeIndex) { return 6 /* Disk */; },
         radius: function (edgeIndex) { return edges[edgeIndex].props.magnitude * sizeFactor; }
     };
     return (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh);
@@ -176,7 +176,7 @@ function getInterClashLabel(structure, clashes, elements) {
     var mag = c.props.magnitude.toFixed(2);
     var dist = c.props.distance.toFixed(2);
     return [
-        "Clash id: " + c.props.id + " | Magnitude: " + mag + " \u212B | Distance: " + dist + " \u212B",
+        "Clash id: ".concat(c.props.id, " | Magnitude: ").concat(mag, " \u212B | Distance: ").concat(dist, " \u212B"),
         (0, label_1.bondLabel)(structure_1.Bond.Location(structure, uA, c.indexA, structure, uB, c.indexB))
     ].join('</br>');
 }

package/lib/commonjs/extensions/rcsb/validation-report/representation.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/commonjs/mol-canvas3d/camera/util.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -25,6 +25,7 @@ declare namespace Viewport {
 export declare function cameraProject(out: Vec4, point: Vec3, viewport: Viewport, projectionView: Mat4): Vec4;
 /**
  * Transform point from screen space to 3D coordinates.
- * The point must have x and y set to 2D window coordinates and z between 0 (near) and 1 (far).
+ * The point must have `x` and `y` set to 2D window coordinates
+ * and `z` between 0 (near) and 1 (far); the optional `w` is not used.
  */
-export declare function cameraUnproject(out: Vec3, point: Vec3, viewport: Viewport, inverseProjectionView: Mat4): Vec3;
+export declare function cameraUnproject(out: Vec3, point: Vec3 | Vec4, viewport: Viewport, inverseProjectionView: Mat4): Vec3;

package/lib/commonjs/mol-canvas3d/camera/util.js CHANGED Viewed

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -52,12 +52,10 @@ exports.Viewport = Viewport;
 })(Viewport || (Viewport = {}));
 exports.Viewport = Viewport;
 //
-var NEAR_RANGE = 0;
-var FAR_RANGE = 1;
 var tmpVec4 = (0, linear_algebra_1.Vec4)();
 /** Transform point into 2D window coordinates. */
 function cameraProject(out, point, viewport, projectionView) {
-    var vX = viewport.x, vY = viewport.y, vWidth = viewport.width, vHeight = viewport.height;
+    var x = viewport.x, y = viewport.y, width = viewport.width, height = viewport.height;
     // clip space -> NDC -> window coordinates, implicit 1.0 for w component
     linear_algebra_1.Vec4.set(tmpVec4, point[0], point[1], point[2], 1.0);
     // transform into clip space
@@ -69,26 +67,27 @@ function cameraProject(out, point, viewport, projectionView) {
         tmpVec4[1] /= w;
         tmpVec4[2] /= w;
     }
-    // transform into window coordinates, set fourth component is (1/clip.w) as in gl_FragCoord.w
-    out[0] = vX + vWidth / 2 * tmpVec4[0] + (0 + vWidth / 2);
-    out[1] = vY + vHeight / 2 * tmpVec4[1] + (0 + vHeight / 2);
-    out[2] = (FAR_RANGE - NEAR_RANGE) / 2 * tmpVec4[2] + (FAR_RANGE + NEAR_RANGE) / 2;
+    // transform into window coordinates, set fourth component to 1 / clip.w as in gl_FragCoord.w
+    out[0] = (tmpVec4[0] + 1) * width * 0.5 + x;
+    out[1] = (1 - tmpVec4[1]) * height * 0.5 + y; // flip Y
+    out[2] = (tmpVec4[2] + 1) * 0.5;
     out[3] = w === 0 ? 0 : 1 / w;
     return out;
 }
 exports.cameraProject = cameraProject;
 /**
  * Transform point from screen space to 3D coordinates.
- * The point must have x and y set to 2D window coordinates and z between 0 (near) and 1 (far).
+ * The point must have `x` and `y` set to 2D window coordinates
+ * and `z` between 0 (near) and 1 (far); the optional `w` is not used.
  */
 function cameraUnproject(out, point, viewport, inverseProjectionView) {
-    var vX = viewport.x, vY = viewport.y, vWidth = viewport.width, vHeight = viewport.height;
-    var x = point[0] - vX;
-    var y = (vHeight - point[1] - 1) - vY;
-    var z = point[2];
-    out[0] = (2 * x) / vWidth - 1;
-    out[1] = (2 * y) / vHeight - 1;
-    out[2] = 2 * z - 1;
+    var x = viewport.x, y = viewport.y, width = viewport.width, height = viewport.height;
+    var px = point[0] - x;
+    var py = (height - point[1] - 1) - y;
+    var pz = point[2];
+    out[0] = (2 * px) / width - 1;
+    out[1] = (2 * py) / height - 1;
+    out[2] = 2 * pz - 1;
     return linear_algebra_1.Vec3.transformMat4(out, out, inverseProjectionView);
 }
 exports.cameraUnproject = cameraUnproject;

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package/lib/commonjs/mol-canvas3d/camera.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -57,8 +57,16 @@ declare class Camera implements ICamera {
     getFocus(target: Vec3, radius: number, up?: Vec3, dir?: Vec3): Partial<Camera.Snapshot>;
     getInvariantFocus(target: Vec3, radius: number, up: Vec3, dir: Vec3): Partial<Camera.Snapshot>;
     focus(target: Vec3, radius: number, durationMs?: number, up?: Vec3, dir?: Vec3): void;
+    /** Transform point into 2D window coordinates. */
     project(out: Vec4, point: Vec3): Vec4;
-    unproject(out: Vec3, point: Vec3): Vec3;
+    /**
+     * Transform point from screen space to 3D coordinates.
+     * The point must have `x` and `y` set to 2D window coordinates
+     * and `z` between 0 (near) and 1 (far); the optional `w` is not used.
+     */
+    unproject(out: Vec3, point: Vec3 | Vec4): Vec3;
+    /** World space pixel size at given `point` */
+    getPixelSize(point: Vec3): number;
     constructor(state?: Partial<Camera.Snapshot>, viewport?: Viewport, props?: Partial<{
         pixelScale: number;
     }>);
@@ -69,7 +77,7 @@ declare namespace Camera {
     /**
      * Sets an offseted view in a larger frustum. This is useful for
      * - multi-window or multi-monitor/multi-machine setups
-     * - jittering the camera position for
+     * - jittering the camera position for sampling
      */
     interface ViewOffset {
         enabled: boolean;

package/lib/commonjs/mol-canvas3d/camera.js CHANGED Viewed

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -11,6 +11,9 @@ var linear_algebra_1 = require("../mol-math/linear-algebra");
 var util_1 = require("./camera/util");
 var transition_1 = require("./camera/transition");
 var rxjs_1 = require("rxjs");
+var tmpPos1 = (0, linear_algebra_1.Vec3)();
+var tmpPos2 = (0, linear_algebra_1.Vec3)();
+var tmpClip = (0, linear_algebra_1.Vec4)();
 var Camera = /** @class */ (function () {
     function Camera(state, viewport, props) {
         if (viewport === void 0) { viewport = util_1.Viewport.create(0, 0, 128, 128); }
@@ -137,12 +140,29 @@ var Camera = /** @class */ (function () {
             this.setState(this.getFocus(target, radius, up, dir), durationMs);
         }
     };
+    /** Transform point into 2D window coordinates. */
     Camera.prototype.project = function (out, point) {
         return (0, util_1.cameraProject)(out, point, this.viewport, this.projectionView);
     };
+    /**
+     * Transform point from screen space to 3D coordinates.
+     * The point must have `x` and `y` set to 2D window coordinates
+     * and `z` between 0 (near) and 1 (far); the optional `w` is not used.
+     */
     Camera.prototype.unproject = function (out, point) {
         return (0, util_1.cameraUnproject)(out, point, this.viewport, this.inverseProjectionView);
     };
+    /** World space pixel size at given `point` */
+    Camera.prototype.getPixelSize = function (point) {
+        // project -> unproject of `point` does not exactly return the same
+        // to get a sufficiently accurate measure we unproject the original
+        // clip position in addition to the one shifted bey one pixel
+        this.project(tmpClip, point);
+        this.unproject(tmpPos1, tmpClip);
+        tmpClip[0] += 1;
+        this.unproject(tmpPos2, tmpClip);
+        return linear_algebra_1.Vec3.distance(tmpPos1, tmpPos2);
+    };
     return Camera;
 }());
 exports.Camera = Camera;

package/lib/commonjs/mol-canvas3d/camera.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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